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Clean Demos for Multiple Alignments
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biojava-structure-gui/src/main/java/demo/DemoCEMC.java renamed to biojava-structure-gui/src/main/java/demo/DemoMultipleMC.java

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import org.biojava.nbio.structure.Atom;
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import org.biojava.nbio.structure.StructureException;
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import org.biojava.nbio.structure.align.ce.CeCPMain;
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import org.biojava.nbio.structure.align.gui.MultipleAlignmentDisplay;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
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import org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain;
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import org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters;
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import org.biojava.nbio.structure.align.util.AtomCache;
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/**
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* @author Aleix Lafita
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*
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*/
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public class DemoCEMC {
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public class DemoMultipleMC {
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public static void main(String[] args) throws IOException, StructureException, InterruptedException, ExecutionException {
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//Protein Kinases (CEMC paper)
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//List<String> names = Arrays.asList("1cdk.A", "1cja.A", "1csn", "1b6c.B", "1ir3.A", "1fgk.A", "1byg.A", "1hck", "1blx.A", "3erk", "1bmk.A", "1kob.A", "1tki.A", "1phk", "1a06");
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//DHFR (Gerstein 1998 paper)
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//List<String> names = Arrays.asList("d1dhfa_", "8dfr", "d4dfra_", "3dfr");
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List<String> names = Arrays.asList("d1dhfa_", "8dfr", "d4dfra_", "3dfr");
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//TIM barrels (MUSTA paper)
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//List<String> names = Arrays.asList("1tim.A", "1vzw", "1nsj", "3tha.A", "4enl", "2mnr", "7tim.A", "1tml", "1btc", "a1piia1", "6xia", "5rub.A", "2taa.B");
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//Helix-bundle (MUSTA paper)
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//List<String> names = Arrays.asList("1bbh.A", "1aep", "1bge.B", "256b.A", "2ccy.A", "2hmz.A", "3ink.C");
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//Calcium Binding (MUSTA paper)
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//List<String> names = Arrays.asList("4cpv", "2scp.A", "2sas", "1top", "1scm.B", "3icb");
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//Serine Rich Proteins SERP (MUSTA paper)
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//GPCRs
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//List<String> names = Arrays.asList("2z73.A", "1u19.A", "4ug2.A", "4xt3", "4or2.A", "3odu.A");
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//Immunoglobulins (MAMMOTH paper)
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List<String> names = Arrays.asList("2hla.B", "3hla.B", "1cd8", "2rhe", "1tlk", "1ten", "1ttf");
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//List<String> names = Arrays.asList("2hla.B", "3hla.B", "1cd8", "2rhe", "1tlk", "1ten", "1ttf");
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//Globins (MAMMOTH, POSA, Gerstein&Levitt and MUSTA papers)
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//List<String> names = Arrays.asList("1mbc", "1hlb", "1thb.A", "1ith.A", "1idr.A", "1dlw", "1kr7.A", "1ew6.A", "1it2.A", "1eco", "3sdh.A", "1cg5.B", "1fhj.B", "1ird.A", "1mba", "2gdm", "1b0b", "1h97.A", "1ash.A", "1jl7.A");
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//Rossman-Fold (POSA paper)
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//Here the multiple structural alignment algorithm comes in place to generate the alignment object
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MultipleMcMain algorithm = new MultipleMcMain();
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MultipleMcParameters params = (MultipleMcParameters) algorithm.getParameters();
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params.setPairwiseAlgorithm(CeCPMain.algorithmName);
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MultipleAlignment result = algorithm.align(atomArrays);
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result.getEnsemble().setStructureNames(names);
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‎biojava-structure/src/main/java/demo/DemoMultipleMC.java‎

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package demo;
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import java.io.IOException;
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import java.util.Arrays;
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import java.util.List;
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import java.util.ArrayList;
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import java.util.concurrent.ExecutionException;
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import org.biojava.nbio.structure.Atom;
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import org.biojava.nbio.structure.StructureException;
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import org.biojava.nbio.structure.align.ce.CeCPMain;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignmentWriter;
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import org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain;
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import org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters;
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import org.biojava.nbio.structure.align.util.AtomCache;
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/**
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* Demo for running the MultipleMC Algorithm on a protein family.
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* For visualizing the results in jmol use the same Demo in the GUI module.
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* Here only the sequence alignment will be displayed.
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* Choose the family by commenting out the protein family names.
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*
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* @author Aleix Lafita
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*
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*/
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public class DemoMultipleMC {
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public static void main(String[] args) throws IOException, StructureException, InterruptedException, ExecutionException {
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//Specify the structures to align
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//ASP-proteinases (CEMC paper)
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//List<String> names = Arrays.asList("3app", "4ape", "2apr", "5pep", "1psn", "4cms", "1bbs.A", "1smr.A", "2jxr.A", "1mpp", "2asi", "1am5");
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//Protein Kinases (CEMC paper)
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//List<String> names = Arrays.asList("1cdk.A", "1cja.A", "1csn", "1b6c.B", "1ir3.A", "1fgk.A", "1byg.A", "1hck", "1blx.A", "3erk", "1bmk.A", "1kob.A", "1tki.A", "1phk", "1a06");
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//DHFR (Gerstein 1998 paper)
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List<String> names = Arrays.asList("d1dhfa_", "8dfr", "d4dfra_", "3dfr");
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//TIM barrels (MUSTA paper)
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//List<String> names = Arrays.asList("1tim.A", "1vzw", "1nsj", "3tha.A", "4enl", "2mnr", "7tim.A", "1tml", "1btc", "a1piia1", "6xia", "5rub.A", "2taa.B");
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//Calcium Binding (MUSTA paper)
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//List<String> names = Arrays.asList("4cpv", "2scp.A", "2sas", "1top", "1scm.B", "3icb");
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//Serine Rich Proteins SERP (MUSTA paper)
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//List<String> names = Arrays.asList("7api.A", "8api.A", "1hle.A", "1ova.A", "2ach.A", "9api.A", "1psi", "1atu", "1kct", "1ath.A", "1att.A");
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//Serine Proteases (MUSTA paper)
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//List<String> names = Arrays.asList("1cse.E", "1sbn.E", "1pek.E", "3prk", "3tec.E");
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//GPCRs
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//List<String> names = Arrays.asList("2z73.A", "1u19.A", "4ug2.A", "4xt3", "4or2.A", "3odu.A");
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//Immunoglobulins (MAMMOTH paper)
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//List<String> names = Arrays.asList("2hla.B", "3hla.B", "1cd8", "2rhe", "1tlk", "1ten", "1ttf");
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//Globins (MAMMOTH, POSA, Gerstein&Levitt and MUSTA papers)
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//List<String> names = Arrays.asList("1mbc", "1hlb", "1thb.A", "1ith.A", "1idr.A", "1dlw", "1kr7.A", "1ew6.A", "1it2.A", "1eco", "3sdh.A", "1cg5.B", "1fhj.B", "1ird.A", "1mba", "2gdm", "1b0b", "1h97.A", "1ash.A", "1jl7.A");
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//Rossman-Fold (POSA paper)
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//List<String> names = Arrays.asList("d1heta2", "d1ek6a_", "d1obfo1", "2cmd", "d1np3a2", "d1bgva1", "d1id1a_", "d1id1a_", "d1oi7a1");
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//Circular Permutations (Bliven CECP paper) - dynamin GTP-ase with CP G-domain
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//List<String> names = Arrays.asList("d1u0la2", "d1jwyb_");
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//Circular Permutations: SAND and MFPT domains
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//List<String> names = Arrays.asList("d2bjqa1", "d1h5pa_", "d1ufna_"); //"d1oqja"
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//Flexible domain family of proteins (FatCat paper?)
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//Ankyrin Repeats
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//List<String> names = Arrays.asList("d1n0ra_", "3ehq.A", "1awc.B"); //ankyrin
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//Load the CA atoms of the structures
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AtomCache cache = new AtomCache();
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List<Atom[]> atomArrays = new ArrayList<Atom[]>();
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for (String name:names) {
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atomArrays.add(cache.getAtoms(name));
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}
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//Here the multiple structural alignment algorithm comes in place to generate the alignment object
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MultipleMcMain algorithm = new MultipleMcMain();
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MultipleMcParameters params = (MultipleMcParameters) algorithm.getParameters();
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params.setPairwiseAlgorithm(CeCPMain.algorithmName);
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MultipleAlignment result = algorithm.align(atomArrays);
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result.getEnsemble().setStructureNames(names);
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//Information about the alignment
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result.getEnsemble().setAlgorithmName(algorithm.getAlgorithmName());
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result.getEnsemble().setVersion(algorithm.getVersion());
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//Output the sequence alignment + transformations
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System.out.println(MultipleAlignmentWriter.toFatCat(result));
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//System.out.println(MultipleAlignmentWriter.toFASTA(result));
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System.out.println(MultipleAlignmentWriter.toTransformMatrices(result));
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}
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}

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